[ci skip] Merge PR 33790

Merge PR bioconda#33790, commits were: 
 * Update meta.yaml
 * Update meta.yaml
 * Update meta.yaml
 * Update meta.yaml
 * Update meta.yaml
 * Update PGCGAP to v1.0.34

Specified dependency version numbers to spend less memory when performing recipe testing.
 * update pgcgap build number

specify the version of all dependences to occupy less memory
 * Update build number

add dependencies
 * Merge branch 'master' into pgcgap3
 * Merge branch 'bioconda:master' into master
 * Update meta.yaml
 * Update meta.yaml
 * Update meta.yaml
 * Update meta.yaml
 * Update build-fail-blacklist

remove PGCGAP
 * Update meta.yaml
 * Merge branch 'master' into pgcgap3
 * Merge branch 'bioconda:master' into master
 * Remove some dependencies to solve error code 137
 * Update PGCGAP to v1.0.33
 * Merge branch 'bioconda:master' into master
 * Merge branch 'bioconda:master' into master
 * Merge branch 'bioconda:master' into master
 * Merge branch 'bioconda:master' into master
 * Merge branch 'master' of https://github.com/liaochenlanruo/bioconda-recipes
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge branch 'bioconda:master' into master
 * Merge branch 'master' of https://github.com/bioconda/bioconda-recipes
 * Merge pull request #3 from bioconda/master

Update local
 * Merge pull request #1 from bioconda/master

Update local

recipes/pgcgap/build.sh

@@ -9,6 +9,7 @@ cp Functions/Pan/grep_cds_aas_from_gff3.pl $PREFIX/bin/
 
 cp Functions/COG/COG.pl $PREFIX/bin/
 cp Functions/COG/COG2020.pl $PREFIX/bin/
+cp Functions/COG/COGdiamond2022.pl $PREFIX/bin/
 cp Functions/COG/get_flag_relative_abundances_table.pl $PREFIX/bin/
 cp Functions/COG/Plot_COG.R $PREFIX/bin/
 cp Functions/COG/Plot_COG_Abundance.R $PREFIX/bin/
@@ -23,12 +24,16 @@ cp Functions/MASH/Plot_MashHeatmap.R $PREFIX/bin/
 cp Functions/Assemble/genome_LenFilter_stats.pl $PREFIX/bin/
 cp Functions/Assemble/get_stats_summary.pl $PREFIX/bin/
 
+cp Functions/ACC/id2seq.pl $PREFIX/bin/
+cp Functions/ACC/get_repeats.pl $PREFIX/bin/
+
 chmod a+x $PREFIX/bin/pgcgap
 chmod a+x $PREFIX/bin/plot_3Dpie.R
 chmod a+x $PREFIX/bin/fmplot.py
 chmod a+x $PREFIX/bin/grep_cds_aas_from_gff3.pl
 chmod a+x $PREFIX/bin/COG.pl
 chmod a+x $PREFIX/bin/COG2020.pl
+chmod a+x $PREFIX/bin/COGdiamond2022.pl
 chmod a+x $PREFIX/bin/get_flag_relative_abundances_table.pl
 chmod a+x $PREFIX/bin/Plot_COG.R
 chmod a+x $PREFIX/bin/triangle2list.pl
@@ -39,5 +44,7 @@ chmod a+x $PREFIX/bin/get_Mash_Matrix.pl
 chmod a+x $PREFIX/bin/Plot_MashHeatmap.R
 chmod a+x $PREFIX/bin/genome_LenFilter_stats.pl
 chmod a+x $PREFIX/bin/get_stats_summary.pl
+chmod a+x $PREFIX/bin/id2seq.pl
+chmod a+x $PREFIX/bin/get_repeats.pl
 
 pgcgap --version

recipes/pgcgap/meta.yaml

@@ -1,65 +1,66 @@
 {% set name = "pgcgap" %}
-{% set version = "1.0.34" %}
+{% set version = "1.0.35" %}
 
 package:
   name: '{{ name }}'
   version: '{{ version }}'
 
 source:
   url: https://github.com/liaochenlanruo/pgcgap/archive/v{{ version }}.tar.gz
-  sha256: ab5373ece8a29262e8f02f5ccdd72262e12dca6381a4139f1164f78d93ef1e25
-
+  sha256: 533030cba1cad4176493fce05ea5223b5e2c0440ed9c60ad408c97d73119ac4a
 
 build:
   number: 0
-  noarch: generic
+  noarch: generic 
 
 requirements:
   host:
     - perl
-    - perl-bioperl >=1.6.924
+    - perl-bioperl >=1.7.8
     - perl-file-tee
     - perl-file-copy-recursive
   run:
-    #- abricate
-    #- canu
-    - openjdk
-    - abyss
-    - prokka
-    - mash
-    #- roary
-    #- orthofinder
-    #- fastani
-    #- fastp
-    - pal2nal
+    - abricate =1.0.1
+    - abyss =2.3.4 # >=2.3.4 important
+    - canu =2.1.1 # <2.2 important
+    - coreutils =9.0
+    - fastani =1.33
+    - fastp =0.23.2
+    - htslib =1.15.1
+    - mamba =0.22.1
+    - mash =2.3 #
+    - matplotlib-base =3.5.1 #
+    - muscle =5.1 # >=5.1 important
+    - numpy =1.21.5 #
+    - openjdk # 8.0.112 important
+#    - java-jdk 8.0.112 # important
+    - orthofinder =2.5.4
+    - panaroo =1.2.10
+    - pandas =1.3.5
+    - pal2nal =14.1
     - perl
-    - perl-bioperl >=1.6.924
-    - perl-file-tee
+#    - perl-bioperl
     - perl-data-dumper
-    - perl-pod-usage
-    - perl-parallel-forkmanager
     - perl-file-copy-recursive
+    - perl-file-tee
+    - perl-parallel-forkmanager
+    - perl-pod-usage
     - perl-posix
-    - htslib
-    #- snippy
-    #- sickle-trim
-    - r-base
+    - prokka >=1.14.5 # important
+#    - python
+    - r-base >=4.1.1
+    - r-corrplot
     - r-ggplot2
     - r-gplots
-    - r-corrplot
-    - trimal
-    - python
-    - matplotlib-base
-    - seaborn
-    - numpy
-    - pandas
-    - biopython
     - r-pheatmap
     - r-plotrix
-    #- unicycler
-    - wget
-    - coreutils
-    - mamba
+    - seaborn =0.11.2
+    - sickle-trim =1.33
+    - snippy =4.6.0 # >=4.6.0 important
+    - snpeff =5.0 # 5.1 error important
+    - trimal =1.4.1
+    - unicycler =0.5.0
+    - wget =1.20.3
 
 test:
   commands: